BioC 2.11: CHECK report for annotate on perceval

Package: annotate

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.36.0.tar.gz

StartedAt: 2013-03-24 22:30:04 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:38:57 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 532.9 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/annotate.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'annotate' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        24.694  0.876  25.759
probesByLL      8.984  0.054   9.078
PWAmat          7.006  0.290   7.407
pm.abstGrep     6.991  0.044   8.378
pm.titles       6.653  0.037   8.170
pm.getabst      5.633  0.047   6.920
blastSequences  1.629  0.106  89.440
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'annotate_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GOusage.Rnw' 
   'annotate.Rnw' 
   'chromLoc.Rnw' 
   'prettyOutput.Rnw' 
   'query.Rnw' 
   'useDataPkgs.Rnw' 
   'useHomology.Rnw' 
   'useProbeInfo.Rnw' 
** testing if installed package can be loaded

* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	3.044	0.088	3.256
GO2heatmap	0.280	0.026	0.307
GOmnplot	0.157	0.014	0.171
HTMLPage-class	0	0	0
LL2homology	0.000	0.001	0.000
PMIDAmat	0.217	0.018	0.236
PWAmat	7.006	0.290	7.407
UniGeneQuery	0.002	0.001	0.004
accessionToUID	0.255	0.040	3.536
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.625	0.110	0.738
blastSequences	1.629	0.106	89.440
buildChromLocation	1.637	0.064	1.718
buildPubMedAbst	0.091	0.005	0.699
chrCats	24.694	0.876	25.759
chromLocation-class	1.610	0.043	1.662
compatibleVersions	0.093	0.015	0.108
dropECode	0.114	0.015	0.128
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.121	0.019	0.141
findNeighbors	0.059	0.013	0.104
genbank	0.243	0.029	1.585
getAnnMap	0.109	0.043	0.165
getEvidence	0.088	0.009	0.097
getGOTerm	0.408	0.028	0.454
getOntology	0.102	0.013	0.115
getPMInfo	1.088	0.009	1.643
getSYMBOL	0.251	0.030	0.285
getSeq4Acc	0.002	0.001	0.280
hasGOannote	0.064	0.010	0.074
hgByChroms	0.019	0.002	0.022
hgCLengths	0.001	0.001	0.003
hgu95Achroloc	0.096	0.008	0.105
hgu95Achrom	0.078	0.007	0.086
hgu95All	0.110	0.011	0.121
hgu95Asym	0.088	0.009	0.099
homoData-class	0.005	0.000	0.004
htmlpage	0.034	0.003	0.036
isValidkey	0	0	0
makeAnchor	0.001	0.000	0.001
organism	1.722	0.042	1.769
p2LL	0	0	0
pm.abstGrep	6.991	0.044	8.378
pm.getabst	5.633	0.047	6.920
pm.titles	6.653	0.037	8.170
pmAbst2HTML	0.164	0.009	0.725
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.002
probesByLL	8.984	0.054	9.078
pubMedAbst-class	0.096	0.006	0.623
pubmed	0.059	0.007	0.828
readGEOAnn	0.001	0.001	0.000
serializeEnv	0.002	0.001	0.004
setRepository	0.001	0.001	0.001
updateSymbolsToValidKeys	0.001	0.000	0.000
usedChromGenes	0.138	0.009	0.147

Summary

Command output